Our knowledge of the pattern of evolution in fungi has increased dramatically over the past 15 years due to (i) the need to know more about fungal evolution, which was created by the increase in the number of immunodeficient humans owing to the tragedy of AIDS and the promise of organ and bone marrow transplantation, (ii) the spread of cladistic theory, and (iii) the technical advances of PCR amplification of DNA and automated DNA sequencing. Some modification of multilocus sequence typing (MLST) may be needed for fungi, where sequence of housekeeping genes may lack the needed variation; microsatellites, for example, may prove more useful and lead to multilocus microsatellite typing (MLMT). Two of every three described fungi are members of the Ascomycota, which is divided into three principal groups, all of which harbor pathogens: Taphrinomycotina, Saccharomycotina, and Pezizomycotina. In Pezizomycotina, pathogens are found in Eurotiomycetes, Sordariomycetes, Chaetothyriomycetes, and Dothidiomycetes. In Eurotiomycetes, pathogens are found in Eurotiales and Onygenales. Basidiomycota comprise three major lineages, one with the rusts and other simple-septate basidiomycetes (Urediniomycetes), a second with the monocot smuts (Ustilaginomycetes), and a third (Hymenomycetes) with the hymenium-forming basidiomycetes, including the “jelly” fungi, bracket fungi, and mushrooms. Molecular phylogenetic studies have shown that neither Zygomycota nor Chytridiomycota is likely to be monophyletic.

Phylogenetic species recognition by congruence of gene genealogies. Within recombining species, different genes have conflicting genealogies. Between genetically isolated species, drift and selection lead to fixation of ancestral polymorphism and congruence of genealogies. The point where congruence gives way to conflict is the point where species are recognized (arrows). Reprinted from reference 194 with permission.

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Figure 1.

Phylogenetic species recognition by congruence of gene genealogies. Within recombining species, different genes have conflicting genealogies. Between genetically isolated species, drift and selection lead to fixation of ancestral polymorphism and congruence of genealogies. The point where congruence gives way to conflict is the point where species are recognized (arrows). Reprinted from reference 194 with permission.

Phylogenetic tree of fungi pathogenic to humans or animals fit to geologic time. A maximum-likelihood phylogeny with an enforced molecular clock based on small-subunit rDNA sequence was used to estimate divergence times for diverse fungi (9), and to this phylogeny were added taxa of commonly encountered pathogenic fungi. Two geologic timescales are used, one reflecting a divergence between animals and fungi at 900 MYA (9) and the other reflecting a divergence at 1,600 MYA (79). Estimates of divergence times are subject to considerable uncertainty, the least of which is due to differences in the estimated time of divergence between animals and fungi (92).

10.1128/9781555815776/f0115-01_thmb.gif

10.1128/9781555815776/f0115-01.gif

Figure 2.

Phylogenetic tree of fungi pathogenic to humans or animals fit to geologic time. A maximum-likelihood phylogeny with an enforced molecular clock based on small-subunit rDNA sequence was used to estimate divergence times for diverse fungi (9), and to this phylogeny were added taxa of commonly encountered pathogenic fungi. Two geologic timescales are used, one reflecting a divergence between animals and fungi at 900 MYA (9) and the other reflecting a divergence at 1,600 MYA (79). Estimates of divergence times are subject to considerable uncertainty, the least of which is due to differences in the estimated time of divergence between animals and fungi (92).

Phylogenetic species recognition applied to species that are exclusively clonal. Exclusively clonal species would not exhibit the change from congruent to conflicting gene genealogies seen in recombining species, which would make species recognition arbitrary. However, if clonal species are uncommon compared to recombining species, then clonal species can be recognized in comparison to their nearest recombining relatives, in this case a sister species. Reprinted from reference 193 with permission.

10.1128/9781555815776/f0117-01_thmb.gif

10.1128/9781555815776/f0117-01.gif

Figure 3.

Phylogenetic species recognition applied to species that are exclusively clonal. Exclusively clonal species would not exhibit the change from congruent to conflicting gene genealogies seen in recombining species, which would make species recognition arbitrary. However, if clonal species are uncommon compared to recombining species, then clonal species can be recognized in comparison to their nearest recombining relatives, in this case a sister species. Reprinted from reference 193 with permission.

107. Kurtzman,C. P., and, C. J.Robnett.1997.Identification of clinically important ascomycetous yeasts based on nucleotide divergence in the 5’ end of the large-subunit (26S) ribosomal DNA gene.J. Clin. Microbiol.35:1216–1223.

215. Untereiner,W. A., and, F. A.Naveau.1999.Molecular systematics of the Herpotrichiellaceae with an assessment of the phylogenetic positions of Exophiala dermatitidis and Phialophora americana.Mycologia91:67–83.